Antigen

Antigen Class

TFs and others

Antigen

JUNB

Cell type

Cell type Class

Breast

Cell type

MDA-MB-231

Primary Tissue

Breast

Site of Extraction

Effusion, Pleural

Tissue Diagnosis

Adenocarcinoma

Sample

source_name

Breast cancer cell line

cell type

MDA-MB-231 cells

transformation status

--

chip antibody

JUNB (Cell Signaling Technology, 3753s)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Cells were dual cross-linking with a mixture of 2 mM each of ethylene glycol bis (succinimidyl succinate) (EGS) and disuccinimidyl glutarate (DSG) and 1% formaldehyde. Chromatin was digested with 60 units MNase (New England Biolabs, M0247S) at 37 0C for 10 minutes and then sonicated using Branson Microtip Sonifier 450 (4X15 second at output 4.5 and duty cycle 60%) to the sizes mostly between 150-500 bp. 50 μg chromatin, antibodies for transcription factors (listed in Table S6), and 15 μl Dynabead protein G (Thermo Fisher Scientific, 10004D) was used for the chromatin immunoprecipitation (ChIP)

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

22990989

Reads aligned (%)

59.4

Duplicates removed (%)

8.3

Number of peaks

40241 (qval < 1E-05)

hg19

Number of total reads

22990989

Reads aligned (%)

59.1

Duplicates removed (%)

9.1

Number of peaks

40189 (qval < 1E-05)